Difference between revisions of "Part:BBa K1104204"

(→‎Where is AhpCp2D1 improved?)
(→‎Usage and Biology)
 
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<partinfo>BBa_K1104204 short</partinfo>
 
<partinfo>BBa_K1104204 short</partinfo>
  
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AhpCp2D1 is a ROS-induced promoter, which is controlled by OxyR (transcription factor) activated by ROS (Reactive Oxygen Species).  
+
AhpCp2D1 is a ROS-induced promoter controlled by OxyR (transcription factor) which is activated by ROS (Reactive Oxygen Species).  
−
[[File: NYMU_A2D1x.png|thumb|600px|center|'''Mutation of ahpC promoter([https://parts.igem.org/Part:BBa_K362001 Part:K362001])''']]
+
[[File: NYMU_A2D1x.png|thumb|400px|center|'''Mutation of ahpC promoter([https://parts.igem.org/Part:BBa_K362001 Part:K362001])''']]
 
AhpCp2D1 is composed of AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205]), reverse promoter DsbGp ([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208]),and AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207]). There are also two dual-TFBSs (Transcription Factor Binding Site) for OxyR binding between AhpCp2 and DsbGp.
 
AhpCp2D1 is composed of AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205]), reverse promoter DsbGp ([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208]),and AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207]). There are also two dual-TFBSs (Transcription Factor Binding Site) for OxyR binding between AhpCp2 and DsbGp.
  
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We annotated it thouroughly based on data from ([http://ecocyc.org/ECOLI/new-image?object=EG11384 Ecocyc]), and found that it contains dsbG coding sequence, AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205]), reverse promoter DsbGp ([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208]),and AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207]), and a PstI cutting site. Thus we improved the promoter by first mutating the PstI cutting site in ahpCp ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001]) and make dsbG coding removed.  
 
We annotated it thouroughly based on data from ([http://ecocyc.org/ECOLI/new-image?object=EG11384 Ecocyc]), and found that it contains dsbG coding sequence, AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205]), reverse promoter DsbGp ([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208]),and AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207]), and a PstI cutting site. Thus we improved the promoter by first mutating the PstI cutting site in ahpCp ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001]) and make dsbG coding removed.  
  
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===Where is AhpCp2D1 improved?===
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===How ahpC ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001]) is improved?===
−
In this part,the PstI cutting site in ahpCp (BBa_K362001) is mutated at one point, and the Dsbg coding sequence is removed.
+
'''In this part,the PstI cutting site in ahpC (BBa_K362001) is mutated at one point, and the Dsbg coding sequence is removed.'''
  
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===How ahpCp ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001]) is improved?===
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Here is the overview about the other ahpC promoter ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001]) related  improvements:
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Here is the overview about the other ahpC promoter ([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001]) improvements:
+
{| border="1" cellpadding="5" cellspacing="0"
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*AhpCp1000 ([https://parts.igem.org/Part:BBa_K1104204 Part:BBa_K1104204]): The PstI cutting site is mutated.
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| AhpCp1000 ([https://parts.igem.org/Part:BBa_K1104203 Part:BBa_K1104203])
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*AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205]): Only one promoter(AhpCp2) and its TFBS.
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| The PstI cutting site is mutated.
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*AhpCpD1 ([https://parts.igem.org/Part:BBa_K1104206 Part:BBa_K1104206]): Bidirectional promoter: AhpCp1 and DsbGp(reverse promoter), and their shared TFBS are left.
+
|-
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*AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207]): Only one promoter(AhpCp1) and its TFBS.
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| AhpCp2D1 ([https://parts.igem.org/Part:BBa_K1104204 Part:BBa_K1104204])
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*DsbGp ([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208]): Only the reverse promoter(DsbGp) and its TFBS.
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| After mutating the PstI cutting site, the truncated coding sequence from the DsbG promoter sequence is removed.
 +
|-
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| AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205])
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| Only one promoter(AhpCp2) and its TFBS.
 +
|-
 +
| AhpCpD1 ([https://parts.igem.org/Part:BBa_K1104206 Part:BBa_K1104206])
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| Bidirectional promoter: AhpCp1 and DsbGp(reverse promoter), and their shared TFBS.
 +
|-
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| AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207])
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| Only one promoter(AhpCp1) and its TFBS.
 +
|}
  
 
===Usage and Biology===
 
===Usage and Biology===
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To enhance the strength , we added a device (more details on [http://2013.igem.org/Team:NYMU-Taipei/Project/Inhibition/Sensor Sensing Nosema] page).
 
To enhance the strength , we added a device (more details on [http://2013.igem.org/Team:NYMU-Taipei/Project/Inhibition/Sensor Sensing Nosema] page).
−
[[File: NYMU_O12.png|frame|center|'''Strenthening device''']]
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[[File: NYMU_O12.png|thumb|500px|center|'''Strenthening device''']]
  
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===Related Parts===
+
Not only for sensing the midgut oxygen stress caused by Nosemasis, in our project, there are some previous iGEM team who used OxyR-induced promoter, such as [http://2010.igem.org/Team:KIT-Kyoto/Parts 2010 KIT-Tokyo team] using it for
 +
the ink of E.coli Pen colorful. And those OxyR-induced promoters relative to the projects.
  
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*ahpC([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001)]
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Since ROS is a natural byproduct of the metabolism and have important roles in cell signaling and homeostasis, the improvement of ROS-induced promoter is useful for sensing some specific conditions. ROS is found to involve in cancer, aging and apoptosis. Thus ROS-induced promoter in the future application can be apply to diagnosis and therapy of certain kinds of physical phenomena or disease.
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**AhpCp1000([https://parts.igem.org/Part:BBa_K1104203 Part:BBa_K1104203])
+
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***[https://parts.igem.org/Part:BBa_K1104242 Part:BBa_K1104243]: AhpCp1000+[https://parts.igem.org/Part:BBa_E0840 E0840]
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**AhpCp2D1([https://parts.igem.org/Part:BBa_K1104204 Part:BBa_K1104204])
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***[https://parts.igem.org/Part:BBa_K1104244 Part:BBa_K1104244]: AhpCp2D1+[https://parts.igem.org/Part:BBa_E0840 E0840]
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**AhpCp2([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205])
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***[https://parts.igem.org/Part:BBa_K1104245 Part:BBa_K1104245]: AhpCp2+[https://parts.igem.org/Part:BBa_E0840 E0840]
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**AhpCpD1([https://parts.igem.org/Part:BBa_K1104206 Part:BBa_K1104206])
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***[https://parts.igem.org/Part:BBa_K1104246 Part:BBa_K1104246]: AhpCpD1+[https://parts.igem.org/Part:BBa_E0840 E0840]
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**AhpCp1([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207])
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***[https://parts.igem.org/Part:BBa_K1104247 Part:BBa_K1104247]: AhpCp1+[https://parts.igem.org/Part:BBa_E0840 E0840]
+
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**DsbGp([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208])
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***[https://parts.igem.org/Part:BBa_K1104248 Part:BBa_K1104248]: DsbGp+[https://parts.igem.org/Part:BBa_E0840 E0840]
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<!-- Add more about the biology of this part here
+
  
 +
Devasagaya, TPA; Tilak JC, Boloor KK, Sane Ketaki S, Ghaskadbi Saroj S, Lele RD (October 2004). "Free Radicals and Antioxidants in Human Health: Current Status and Future Prospects". Journal of Association of Physicians of India (JAPI) 52: 796.
 +
 +
===Related Parts===
 +
{| border="1" cellpadding="5" cellspacing="0"
 +
| colspan=6 align="center"| ahpC([https://parts.igem.org/Part:BBa_K362001 Part:BBa_K362001)]
 +
|-
 +
| AhpCp1000 ([https://parts.igem.org/Part:BBa_K1104203 Part:BBa_K1104203])
 +
| AhpCp2D1 ([https://parts.igem.org/Part:BBa_K1104204 Part:BBa_K1104204])
 +
| AhpCp2 ([https://parts.igem.org/Part:BBa_K1104205 Part:BBa_K1104205])
 +
| AhpCpD1 ([https://parts.igem.org/Part:BBa_K1104206 Part:BBa_K1104206])
 +
| AhpCp1 ([https://parts.igem.org/Part:BBa_K1104207 Part:BBa_K1104207])
 +
| DsbGp ([https://parts.igem.org/Part:BBa_K1104208 Part:BBa_K1104208])
 +
|-
 +
| AhpCp1000+[https://parts.igem.org/Part:BBa_E0840 E0840] ([https://parts.igem.org/Part:BBa_K1104243 Part:BBa_K1104243])
 +
| AhpCp2D1+[https://parts.igem.org/Part:BBa_E0840 E0840] ([https://parts.igem.org/Part:BBa_K1104244 Part:BBa_K1104244])
 +
| AhpCp2+[https://parts.igem.org/Part:BBa_E0840 E0840] ([https://parts.igem.org/Part:BBa_K1104245 Part:BBa_K1104245])
 +
| AhpCpD1+[https://parts.igem.org/Part:BBa_E0840 E0840] ([https://parts.igem.org/Part:BBa_K1104246 Part:BBa_K1104246])
 +
| AhpCp1+[https://parts.igem.org/Part:BBa_E0840 E0840] ([https://parts.igem.org/Part:BBa_K1104247 Part:BBa_K1104247])
 +
| --
 +
|}
 
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>

Latest revision as of 16:17, 26 October 2013

AhpCp2D1

AhpCp2D1 is a ROS-induced promoter controlled by OxyR (transcription factor) which is activated by ROS (Reactive Oxygen Species).

Mutation of ahpC promoter(Part:K362001)

AhpCp2D1 is composed of AhpCp2 (Part:BBa_K1104205), reverse promoter DsbGp (Part:BBa_K1104208),and AhpCp1 (Part:BBa_K1104207). There are also two dual-TFBSs (Transcription Factor Binding Site) for OxyR binding between AhpCp2 and DsbGp.

Improvement

We improved a BioBrick Part: ahpC promoter (Part:K362001) designed by [http://2010.igem.org/Team:KIT-Kyoto/Parts 2010 KIT-Tokyo team]. On PartRegistry, the complex part(according to [http://ecocyc.org/ECOLI/new-image?object=EG11384 Ecocyc]) composition contains hybrid promoters, shared TFBS (Transcription Factor Binding Site), and reverse promoter DsbG. In this part AhpCp2D1, we succesfully mutated the PstI cutting site (ctgcag->ctacag) of ahpC promoter (Part:K362001), and removed the dsbG coding sequence.

ahpC promoter, as well as its improvement, can be activated by OxyR (Part:BBa_K1104200).

We annotated it thouroughly based on data from ([http://ecocyc.org/ECOLI/new-image?object=EG11384 Ecocyc]), and found that it contains dsbG coding sequence, AhpCp2 (Part:BBa_K1104205), reverse promoter DsbGp (Part:BBa_K1104208),and AhpCp1 (Part:BBa_K1104207), and a PstI cutting site. Thus we improved the promoter by first mutating the PstI cutting site in ahpCp (Part:BBa_K362001) and make dsbG coding removed.

How ahpC (Part:BBa_K362001) is improved?

In this part,the PstI cutting site in ahpC (BBa_K362001) is mutated at one point, and the Dsbg coding sequence is removed.

Here is the overview about the other ahpC promoter (Part:BBa_K362001) related improvements:

AhpCp1000 (Part:BBa_K1104203) The PstI cutting site is mutated.
AhpCp2D1 (Part:BBa_K1104204) After mutating the PstI cutting site, the truncated coding sequence from the DsbG promoter sequence is removed.
AhpCp2 (Part:BBa_K1104205) Only one promoter(AhpCp2) and its TFBS.
AhpCpD1 (Part:BBa_K1104206) Bidirectional promoter: AhpCp1 and DsbGp(reverse promoter), and their shared TFBS.
AhpCp1 (Part:BBa_K1104207) Only one promoter(AhpCp1) and its TFBS.

Usage and Biology

We designed circuit fighting against Nosema ceranae. After Nosema ceranae infected midgut cells of bees, and Bee. coli should sense the pathogen first before the following circuit(fighting against Nosema ceranae)is triggered, and substance such as Defensin(Part:BBa_K1104300), Abaesin(Part:BBa_K1104301) (more details on [http://2013.igem.org/Team:NYMU-Taipei/Project/Inhibition/Killing Killing Nosema] page) in the following circuit will express.

To enhance the strength , we added a device (more details on [http://2013.igem.org/Team:NYMU-Taipei/Project/Inhibition/Sensor Sensing Nosema] page).

Strenthening device

Not only for sensing the midgut oxygen stress caused by Nosemasis, in our project, there are some previous iGEM team who used OxyR-induced promoter, such as [http://2010.igem.org/Team:KIT-Kyoto/Parts 2010 KIT-Tokyo team] using it for the ink of E.coli Pen colorful. And those OxyR-induced promoters relative to the projects.

Since ROS is a natural byproduct of the metabolism and have important roles in cell signaling and homeostasis, the improvement of ROS-induced promoter is useful for sensing some specific conditions. ROS is found to involve in cancer, aging and apoptosis. Thus ROS-induced promoter in the future application can be apply to diagnosis and therapy of certain kinds of physical phenomena or disease.

Devasagaya, TPA; Tilak JC, Boloor KK, Sane Ketaki S, Ghaskadbi Saroj S, Lele RD (October 2004). "Free Radicals and Antioxidants in Human Health: Current Status and Future Prospects". Journal of Association of Physicians of India (JAPI) 52: 796.

Related Parts

ahpC(Part:BBa_K362001)
AhpCp1000 (Part:BBa_K1104203) AhpCp2D1 (Part:BBa_K1104204) AhpCp2 (Part:BBa_K1104205) AhpCpD1 (Part:BBa_K1104206) AhpCp1 (Part:BBa_K1104207) DsbGp (Part:BBa_K1104208)
AhpCp1000+E0840 (Part:BBa_K1104243) AhpCp2D1+E0840 (Part:BBa_K1104244) AhpCp2+E0840 (Part:BBa_K1104245) AhpCpD1+E0840 (Part:BBa_K1104246) AhpCp1+E0840 (Part:BBa_K1104247) --

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]